BioSilicoList2

BioSilicoList

A comprehensive list of available in silico tools for genetics and genomics

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Sequence databases and analysis tools

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*Databases

UCSC Human http://genome.ucsc.edu/cgi-bin/hgGateway

Ensembl Human http://www.ensembl.org/Homo_sapiens/index.html

NCBI Human http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9606

Genecards http://genecards.org/

KEGG pathway http://www.genome.jp/kegg/pathway.html

Gene Ontology http://www.geneontology.org/

NCBI Homologene http://www.ncbi.nlm.nih.gov/sites/entrez?db=homologene

flybase http://flybase.bio.indiana.edu/

Homophila http://superfly.ucsd.edu/homophila/

flyatlas http://www.flyatlas.org/

Comparative Toxicogenomics Database http://ctd.mdibl.org/

Gene Aging Nexus http://gan.usc.edu/public/index.jsp

SynDB http://syndb.cbi.pku.edu.cn/sdb_index.php

WikiPathways http://www.wikipathways.org/index.php/WikiPathways

IntAct http://www.ebi.ac.uk/intact

NCBI BioSystems http://www.ncbi.nlm.nih.gov/biosystems

Pathway Interaction Database http://pid.nci.nih.gov/browse_pathways.shtml#NCI-Nature

REBASE http://rebase.neb.com/rebase/rebase.html

RTPrimerDB http://medgen.ugent.be/rtprimerdb/index.php

Quantitative PCR Primer Database (QPPD) http://web.ncifcrf.gov/rtp/gel/primerdb/

Primer Bank http://pga.mgh.harvard.edu/primerbank/

qPrimerDepot http://primerdepot.nci.nih.gov/

Satellog Database http://satellog.bcgsc.ca/

GeneCards Hot Genes http://www.genecards.org/hotCards.shtml

BioNumbers http://bionumbers.hms.harvard.edu/default.aspx

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*Servers/Programs

UCSC Blat http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

NCBI Blast http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9606

Primer3 http://frodo.wi.mit.edu/

Clustal W http://www.ebi.ac.uk/Tools/clustalw2/index.html

Reverse complement http://www.bioinformatics.org/sms/rev_comp.html

NEBcutter http://tools.neb.com/NEBcutter2/index.php

reverse complement http://arbl.cvmbs.colostate.edu/molkit/manip/

MFEprimer http://biocompute.bmi.ac.cn/MFEprimer/

PrimerStation http://ps.cb.k.u-tokyo.ac.jp/index.html

IDT OligoAnalyzer http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/

BioEdit http://www.mbio.ncsu.edu/bioedit/bioedit.html

pDRAW32 http://www.acaclone.com/

Protein Movie Generator http://bioserv.rpbs.jussieu.fr/~autin/cgi-bin/PMG

geNorm http://medgen.ugent.be/~jvdesomp/genorm/

WebLogo http://weblogo.berkeley.edu/logo.cgi

Venny http://bioinfogp.cnb.csic.es/tools/venny/index.html

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*Data Mining in Genomics

Taverna http://taverna.sourceforge.net/

Galaxy http://g2.trac.bx.psu.edu/wiki

BioMart http://www.biomart.org/biomart/martview

myExperiment http://www.myexperiment.org/workflows

iTools http://cms.loni.ucla.edu/iTools/index.aspx

Orange http://www.ailab.si/orange/

Weka http://www.cs.waikato.ac.nz/~ml/weka/index.html

BioWeka http://bioweka.sourceforge.net/

BioMoby http://biomoby.open-bio.org/index.php/what-is-moby/publications

Remora http://lipm-bioinfo.toulouse.inra.fr/remora/cgi/remora.cgi

Seahawk http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Seahawk.html

Sight http://www.bioinformatics.org/jSight/

Mobyle http://mobyle.pasteur.fr/cgi-bin/portal.py

ENDEAVOUR http://homes.esat.kuleuven.be/~bioiuser/endeavour/endeavour.php

ToppGene http://toppgene.cchmc.org/prioritization.jsp

Geneseeker http://www.cmbi.ru.nl/GeneSeeker/basic_form.html

G2D http://www.ogic.ca/projects/g2d_2/

Prospectr http://www.genetics.med.ed.ac.uk/prospectr/

SNOW http://snow.bioinfo.cipf.es/cgi-bin/snow.cgi

ToppNet http://toppgene.cchmc.org/network.jsp

GeneDistiller http://www.genedistiller.org/

Cipher http://bioinfo.au.tsinghua.edu.cn/cipher/cipher_search.php

GeneWanderer http://compbio.charite.de/genewanderer/GeneWanderer

TrAPSS2 http://putt.eng.uiowa.edu/trapss_research.html

DrugBank http://www.drugbank.ca/

Network Workbench http://nwb.slis.indiana.edu/index.html

iHOP http://www.ihop-net.org/UniPub/iHOP/

UniHI http://theoderich.fb3.mdc-berlin.de:8080/unihi/index

Chilibot http://www.chilibot.net/

SCAN http://scan.bsd.uchicago.edu/newinterface/about.html

HEFalMp http://sonorus.princeton.edu/hefalmp/

JSquid http://jsquid.sbc.su.se/

VECT http://www.complex.iastate.edu/download/Vect/index.html

KGG http://bioinfo.hku.hk:13080/kggweb/

GeneALaCart http://genecards.org/BatchQueries/index.php

EMMA http://www.emmanet.org/mutant_types.php

SNPExpress database http://people.genome.duke.edu/~dg48/SNPExpress/1_database.php

eQTL imputation http://www.sph.umich.edu/csg/liang/imputation/